Ultrahigh-resolution crystal structures of Z-DNA in complex with Mn ²⁺ and Zn²⁺ ions

Authors:

• Paweł Michał Drożdżal,
• Mirosław Gilski,
• Ryszard Kierzek,
• Lechosław Łomozik,
• Mariusz Jaskólski

Abstract

X-ray crystal structures of the spermine⁴⁺ form of the Z-DNA duplex with the self-complementary d(CG)3 sequence in complexes with Mn ²⁺ and Zn²⁺ cations have been determined at the ultrahigh resolutions of 0.75 and 0.85 14;Å, respectively. Stereochemical restraints were only used for the sperminium cation (in both structures) and for nucleotides with dual conformation in the Zn²⁺ complex. The Mn ²⁺ and Zn²⁺ cations at the major site, designated M ²⁺(1), bind at the N7 position of G6 by direct coordination. The coordination geometry of this site was octahedral, with complete hydration shells. An additional Zn²⁺(2) cation was bis-coordinated in a tetrahedral fashion by the N7 atoms of G10 and G12 from a symmetry-related molecule. The coordination distances of Zn²⁺(1) and Zn ²⁺(2) to the O6 atom of the guanine residues were 3.613 14;(6) and 3.258 14;(5) 14;Å, respectively. Moreover, a chloride ion was also identified in the coordination sphere of Zn²⁺(2). Alternate conformations were observed in the Z-DNA-Zn²⁺ structure not only at internucleotide linkages but also at the terminal C3′ - OH group of G12. The conformation of the sperminium chain in the Z-DNA-Mn²⁺ complex is similar to the spermine⁴⁺ conformation in analogous Z-DNA-Mg ²⁺ structures. In the Z-DNA-Zn²⁺ complex the sperminium cation is disordered and partially invisible in electron-density maps. In the Z-DNA-Zn²⁺ complex the sperminium cation only interacts with the phosphate groups of the Z-DNA molecules, while in the Z-DNA-Mn²⁺ structure it forms hydrogen bonds to both the phosphate groups and DNA bases. © 2013 International Union of Crystallography.